For a good cutting tool, you cannot beat a dremel. However, it sounds as though you are a virgin when it comes to using one, so make sure to have some sandpaper ready to smooth out your cuts. Don't worry, there is no shame in that: my dremel skills rank right up their with accurately predicting the path of purely theoretical particles. I need sandpaper myself. Make sure, as well, to get a lot of practice using that dremel on hard plastic before you get near the mobo. That would be very risky without practice.
Materialwise, I recommend plexiglass or acrylic. I think you would have to order acrylic online, but plexiglass you can usually purchase at any large hardware store. I will also warn you, unless you're serious about cutting the mobo in half and connecting it back together, this will probably be the most difficult part of your custom work. I do not have any experience with this, but I am speaking from reading the difficulties other people have had.
From what I have seen, most people use special metal "joiners" (don't know the real term) on the corners with screws. It that is not avaliable, I would imagine clear super glue MIGHT work... but that would end up looking sloppy, I think.
You'll definately have to look up some tutorials on working with plexiglass. So I say good luck, and God speed!
- Greg